RetrogeneDB ID: retro_cjac_1776

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:38267840..38268464(+)
• Located in intron of: ENSCJAG00000031434

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000017797
• Aliases: None
• Description: None

Sequence

>retro_cjac_1776
AAAATGGCTGGACTGGACAAGCAGGCAAAGCTGAGTGATCTACAGACTGCGACCGCGGGGTCCTTTGCCTCTGCATTCGC
CTCGTTGGCTCTCTGCCCCACTGAGCTTGTGAAGTGCCGGCTACAGACCATGTATGAAATGGAGATGTCAGGGAAGATAG
CAAAAAGCCATAATACAATTTGGTCTGTCGTGAAGAACATCCTTAAAAAGGATGGCCCCTTGGGCTTCTACCACGGACTC
TCCAGTACTCTACTTCAAGAAGTACCGGGTTACTTCTTTTTCTTTGGTGGCTATGAACTGAGCCGATCGTTTTTTGCATC
AGGGAGATCAAAAGATGAACTAGGCCCTGTCCATTTGATGTTAAGTGGCGGAGTTGCTGGAATTTCTCTCTGGCTTGTCG
TGTTCCCAGTGGATTGTATTAAATCCAGAATTCAGGTTCTTTCTATGCATGGAAAACAGGCAGGATTTGTTGGTACCCTC
TTAAGTGTCGCAAAAAATGAAGGAATAGCAGCCTTATATTCTGGACTGACAGCTACTATGATTCGAGCAGTCCCTGCAAA
TGGGGCGCTGTTTGTGGCCTATGAATACAGCAGGAAGATGATGATGAGCCAGCTGGAAGCATAC

Alignment

ORF - retro_cjac_1776 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.1 %
• Parental protein coverage: 86.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVAGLDKQAKLSDLQNAAAGSFASAFAALVLCPTELVKCRLQTMYEMETSGKIAKSQNTVWSVIKSVLRK
          K.AGLDKQAKLSDLQ.A.AGSFASAFA.L.LCPTELVKCRLQTMYEME.SGKIAKS.NT.WSV.K..L.K
Retrocopy KMAGLDKQAKLSDLQTATAGSFASAFASLALCPTELVKCRLQTMYEMEMSGKIAKSHNTIWSVVKNILKK

Parental  DGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGRSKDELGPVPLVLSGGVGGICLWLAVYPVDCI
          DGPLGFYHGLSSTLL.EVPGYFFFFGGYELSRSFFASGRSKDELGPV.L.LSGGV.GI.LWL.V.PVDCI
Retrocopy DGPLGFYHGLSSTLLQEVPGYFFFFGGYELSRSFFASGRSKDELGPVHLMLSGGVAGISLWLVVFPVDCI

Parental  KSRIQVLSMSGKQAGFIRTFISVVKNEGIMALYSGLKPTMIRAFPANGALFLAYEYSRKLMMSQLEAY
          KSRIQVLSM.GKQAGF..T..SV.KNEGI.ALYSGL..TMIRA.PANGALF.AYEYSRK.MMSQLEAY
Retrocopy KSRIQVLSMHGKQAGFVGTLLSVAKNEGIAALYSGLTATMIRAVPANGALFVAYEYSRKMMMSQLEAY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.02 RPM	3.62 RPM
SRP051959_heart	0.05 RPM	0.82 RPM
SRP051959_kidney	0.00 RPM	0.69 RPM
SRP051959_liver	0.02 RPM	43.17 RPM
SRP051959_lung	0.05 RPM	1.15 RPM
SRP051959_lymph_node	0.00 RPM	0.25 RPM
SRP051959_skeletal_muscle	0.04 RPM	1.51 RPM
SRP051959_spleen	0.00 RPM	0.46 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1776 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1776 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1776 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017797	1 retrocopy	retro_cjac_1776 ,
Cavia porcellus	ENSCPOG00000005570	2 retrocopies	retro_cpor_105, retro_cpor_107,
Equus caballus	ENSECAG00000007666	1 retrocopy	retro_ecab_72,
Homo sapiens	ENSG00000102743	1 retrocopy	retro_hsap_44,
Gorilla gorilla	ENSGGOG00000025261	1 retrocopy	retro_ggor_2294,
Microcebus murinus	ENSMICG00000007218	1 retrocopy	retro_mmur_18,
Macaca mulatta	ENSMMUG00000022585	1 retrocopy	retro_mmul_199,
Nomascus leucogenys	ENSNLEG00000001185	1 retrocopy	retro_nleu_1704,
Otolemur garnettii	ENSOGAG00000009380	1 retrocopy	retro_ogar_490,
Pongo abelii	ENSPPYG00000005307	1 retrocopy	retro_pabe_82,
Pan troglodytes	ENSPTRG00000005809	1 retrocopy	retro_ptro_2303,
Pteropus vampyrus	ENSPVAG00000010393	1 retrocopy	retro_pvam_15,
Ictidomys tridecemlineatus	ENSSTOG00000007840	1 retrocopy	retro_itri_726,
Tupaia belangeri	ENSTBEG00000017239	1 retrocopy	retro_tbel_4583,